☰ Navigation Tabs
Crystal structure of HP1gamma chromoshadow domain in complex with KAP1 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KUP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 1.0 M LiCl2, 0.1 M citrate buffer pH 4.0, and 20% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.56 52.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.726 α = 90 b = 60.726 β = 90 c = 43.042 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 200K 2021-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.77 50 97 0.041 0.043 0.012 0.999 25.8 11.7 9004
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.8 85.7 0.362 0.39 0.14 0.939 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.77 26.31 8474 452 96.75 0.20795 0.20646 0.2145 0.23587 0.2389 RANDOM 30.352
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.32 0.16 0.32 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.177 r_long_range_B_refined 6.532 r_long_range_B_other 6.431 r_dihedral_angle_1_deg 6.132 r_scangle_other 5.235 r_dihedral_angle_2_deg 5.079 r_mcangle_it 3.616 r_mcangle_other 3.611 r_scbond_it 3.33 r_scbond_other 3.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.177 r_long_range_B_refined 6.532 r_long_range_B_other 6.431 r_dihedral_angle_1_deg 6.132 r_scangle_other 5.235 r_dihedral_angle_2_deg 5.079 r_mcangle_it 3.616 r_mcangle_other 3.611 r_scbond_it 3.33 r_scbond_other 3.227 r_mcbond_it 2.446 r_mcbond_other 2.444 r_angle_refined_deg 1.758 r_angle_other_deg 0.618 r_chiral_restr 0.095 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 552 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction